2E6O - JenaLib

NMR Structure - model 1

NMR Structure - all models

collapse

expand

NMR Structure - model 1 (Jmol Viewer)

NMR Structure - all models (Jmol Viewer)

Description

Title :   SOLUTION STRUCTURE OF THE HMG BOX DOMAIN FROM HUMAN HMG-BOX TRANSCRIPTION FACTOR 1

Authors :   X. R. Qin, F. Hayashi, S. Yokoyama, Riken Structural Genomics/Proteomics Initiative (Rsgi)

Date :   28 Dec 06 (Deposition) - 03 Jul 07 (Release) - 24 Feb 09 (Revision)

Method :   SOLUTION NMR

Resolution :   NOT APPLICABLE

Chains :   NMR Structure  : A  (20x)

Keywords :   Hmg-Box Domain, Hmg Box Containing Protein 1, Hmg-Box Transcription Factor 1, High Mobility Group Box Transcription Factor 1, Structural Genomics, Nppsfa, National Project On Protein Structural And Functional Analyses, Riken Structural Genomics/Proteomics Initiative, Rsgi, Transcription, Cell Cycle (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )

Reference :   X. R. Qin, F. Hayashi, S. Yokoyama
Solution Structure Of The Hmg Box Domain From Human Hmg-Box Transcription Factor 1
To Be Published
PubMed: search
(for further references see the PDB file header)

Compounds

Molecule 1 - HMG BOX-CONTAINING PROTEIN 1
	Chains	:	A
	Engineered	:	YES
	Expression System Plasmid	:	P060206-06
	Expression System Vector Type	:	PLASMID
	Fragment	:	HMG-BOX
	Gene	:	HBP1
	Organism Common	:	HUMAN
	Organism Scientific	:	HOMO SAPIENS
	Organism Taxid	:	9606
	Other Details	:	CELL FREE PROTEIN SYNTHESIS
	Synonym	:	HMG BOX TRANSCRIPTION FACTOR 1, HIGH MOBILITY GROUP BOX TRANSCRIPTION FACTOR 1

Structural Features

Chains, Units


NMR Structure (20x)	:

Summary Information (see also Sequences/Alignments below)

Ligands, Modified Residues, Ions (0, 0)

(no "Ligand,Modified Residues,Ions" information available for 2E6O)

Sites (0, 0)

(no "Site" information available for 2E6O)

SS Bonds (0, 0)

(no "SS Bond" information available for 2E6O)

Cis Peptide Bonds (0, 0)

(no "Cis Peptide Bond" information available for 2E6O)

Sequence-Structure Mapping

SAPs(SNPs)/Variants (0, 0)

(no "SAP(SNP)/Variant" information available for 2E6O)

PROSITE Motifs (1, 1)

NMR Structure (1, 1)

	PROSITE			UniProtKB		PDB
No.	ID	AC	Description	ID	Location	Count	Location
1	HMG_BOX_2	PS50118	HMG boxes A and B DNA-binding domains profile.	HBP1_HUMAN	434-502	1	A:18-86

Exons (2, 2)

NMR Structure (2, 2)

	ENSEMBL					UniProtKB			PDB
No.	Transcript ID	Exon	Exon ID	Genome Location	Length	ID	Location	Length	Count	Location	Length
1.1d	ENST00000222574	1d	ENSE00001374924	chr7:106809460-106809630	171	HBP1_HUMAN	-	0	0	-	-
1.5e	ENST00000222574	5e	ENSE00000881751	chr7:106820324-106820507	184	HBP1_HUMAN	1-57	57	0	-	-
1.6e	ENST00000222574	6e	ENSE00000715119	chr7:106822818-106823046	229	HBP1_HUMAN	57-133	77	0	-	-
1.7	ENST00000222574	7	ENSE00000715126	chr7:106826246-106826387	142	HBP1_HUMAN	133-180	48	0	-	-
1.8a	ENST00000222574	8a	ENSE00000715132	chr7:106826806-106826917	112	HBP1_HUMAN	181-218	38	0	-	-
1.9	ENST00000222574	9	ENSE00000715138	chr7:106827014-106827126	113	HBP1_HUMAN	218-255	38	0	-	-
1.10	ENST00000222574	10	ENSE00000715143	chr7:106829737-106829893	157	HBP1_HUMAN	256-308	53	0	-	-
1.11b	ENST00000222574	11b	ENSE00000715147	chr7:106830618-106830762	145	HBP1_HUMAN	308-356	49	0	-	-
1.12b	ENST00000222574	12b	ENSE00000715151	chr7:106836279-106836596	318	HBP1_HUMAN	356-462	107	1	A:1-46 (gaps)	62
1.13b	ENST00000222574	13b	ENSE00001432769	chr7:106840605-106840746	142	HBP1_HUMAN	462-509	48	1	A:46-87	42
1.14e	ENST00000222574	14e	ENSE00001829379	chr7:106841859-106842974	1116	HBP1_HUMAN	510-514	5	0	-	-

Sequences/Alignments

NMR Structure

Reformat:	Number of residues per line = ('0' or empty: single-line sequence representation)
	Number of residues per labelling interval =
	UniProt sequence: complete aligned part

Show mapping:	SCOP domains	CATH domains	Pfam domains	Secondary structure (by author)
	SAPs(SNPs)	PROSITE motifs	Exons
	(details for a mapped element are shown in a popup box when the mouse pointer rests over it)

Chain A from PDB  Type:PROTEIN  Length:87
 aligned with HBP1_HUMAN | O60381 from UniProtKB/Swiss-Prot  Length:514

    Alignment length:103
                                   410       420       430       440       450       460       470       480       490       500   
           HBP1_HUMAN   401 GSPGSSQLSSNSLYAKAVKNHSSGTVSATSPNKCKRPMNAFMLFAKKYRVEYTQMYPGKDNRAISVILGDRWKKMKNEERRMYTLEAKALAEEQKRLNPDCWK 503
               SCOP domains d2e6oa                _ A: automated matches                                                            SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ......----------------................hhhhhhhhhhhhhhhhhh...hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh..... Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ---------------------------------HMG_BOX_2  PDB: A:18-86 UniProt: 434-502                             - PROSITE
           Transcript 1 (1) Exon 1.12b  PDB: A:1-46 (gaps) UniProt: 356-462 [INCOMPLETE]  ----------------------------------------- Transcript 1 (1)
           Transcript 1 (2) -------------------------------------------------------------Exon 1.13b  PDB: A:46-87 UniProt: 462-509  Transcript 1 (2)
                 2e6o A   1 GSSGSS----------------GGTVSATSPNKCKRPMNAFMLFAKKYRVEYTQMYPGKDNRAISVILGDRWKKMKNEERRMYTLEAKALAEEQKRLNPDCWK  87
                                 |   -         -  |     14        24        34        44        54        64        74        84   
                                 6                7

Legend:		→ Mismatch	(orange background)
	-	→ Gap	(green background, '-', border residues have a numbering label)
		→ Modified Residue	(blue background, lower-case, 'x' indicates undefined single-letter code, labelled with number + name)
	x	→ Chemical Group	(purple background, 'x', labelled with number + name, e.g. ACE or NH2)
	extra numbering lines below/above indicate numbering irregularities and modified residue names etc., number ends below/above '\|'

Classification and Annotation

SCOP Domains (1, 1)

NMR Structure

Classes(

)

Folds(

)

Superfamilies( (-)

)

Families(

)

Protein Domains( (-)

)

Organisms( (-)

)

Class: All alpha proteins (14657)

Fold: HMG-box (49)

Superfamily: HMG-box (49)

Family: automated matches (6)

Protein domain: automated matches (6)

Human (Homo sapiens) [TaxId: 9606] (3)

d2e6oa_

CATH Domains (0, 0)

(no "CATH Domain" information available for 2E6O)

Pfam Domains (0, 0)

(no "Pfam Domain" information available for 2E6O)

Gene Ontology (10, 10)

NMR Structure(hide GO term definitions)

Chain A (HBP1_HUMAN | O60381)

molecular function
	GO:0003677	DNA binding	Any molecular function by which a gene product interacts selectively and non-covalently with DNA (deoxyribonucleic acid).
	GO:0003723	RNA binding	Interacting selectively and non-covalently with an RNA molecule or a portion thereof.
	GO:0005515	protein binding	Interacting selectively and non-covalently with any protein or protein complex (a complex of two or more proteins that may include other nonprotein molecules).
biological process
	GO:0016055	Wnt signaling pathway	The series of molecular signals initiated by binding of a Wnt protein to a frizzled family receptor on the surface of the target cell and ending with a change in cell state.
	GO:0007050	cell cycle arrest	A regulatory process that halts progression through the cell cycle during one of the normal phases (G1, S, G2, M).
	GO:0043268	positive regulation of potassium ion transport	Any process that activates or increases the frequency, rate or extent of the directed movement of potassium ions (K+) into, out of or within a cell, or between cells, by means of some agent such as a transporter or pore.
	GO:0006355	regulation of transcription, DNA-templated	Any process that modulates the frequency, rate or extent of cellular DNA-templated transcription.
	GO:0006351	transcription, DNA-templated	The cellular synthesis of RNA on a template of DNA.
cellular component
	GO:0005654	nucleoplasm	That part of the nuclear content other than the chromosomes or the nucleolus.
	GO:0005634	nucleus	A membrane-bounded organelle of eukaryotic cells in which chromosomes are housed and replicated. In most cells, the nucleus contains all of the cell's chromosomes except the organellar chromosomes, and is the site of RNA synthesis and processing. In some species, or in specialized cell types, RNA metabolism or DNA replication may be absent.

Visualization

Interactive Views

NMR Structure
	Complete Structure
		Jena3D(integrated viewing of ligand, site, SAP, PROSITE, SCOP information)
		WebMol \| AstexViewer[tm]@PDBe (Java Applets, require no local installation except for Java; loading may be slow)
		STRAP (Java WebStart application, automatic local installation, requires Java; full application with system access!)
		RasMol (require local installation)
		Molscript (VRML) (requires installation of a VRML viewer; select preferred view via VRML and generate a mono or stereo PDF format file)

	Ligands, Modified Residues, Ions
(no "Ligands, Modified Residues, Ions" information available for 2e6o)

	Sites
(no "Sites" information available for 2e6o)

	Cis Peptide Bonds
(no "Cis Peptide Bonds" information available for 2e6o)

Still Images

Jmol
	protein: cartoon or spacefill or dots and stick; nucleic acid: cartoon and stick; ligands: spacefill; active site: stick [ NMR Structure - model 1 PNG format \| NMR Structure - all models PNG format ](automatic orientation, automatically generated)
Molscript
	protein, nucleic acid: cartoon; ligands: spacefill; active site: ball and stick [ mono PDF format \| stereo PDF format ](default orientation, automatically generated)

Databases and Analysis Tools

Databases

Access by PDB/NDB ID
	2e6o
		Family and Domain Information	:	ProDom \| SYSTERS
		General Structural Information	:	GlycoscienceDB \| MMDB \| NDB \| OCA \| PDB \| PDBe \| PDBj \| PDBsum \| PDBWiki \| PQS \| PROTEOPEDIA
		Orientation in Membranes	:	OPM
		Protein Surface	:	SURFACE
		Secondary Structure	:	DSSP (structure derived) \| HSSP (homology derived)
		Structural Genomics	:	GeneCensus
		Structural Neighbours	:	CE \| VAST
		Structure Classification	:	CATH \| Dali \| SCOP
		Validation and Original Data	:	BMRB Data View \| BMRB Restraints Grid \| EDS \| PROCHECK \| RECOORD \| WHAT_CHECK

Access by UniProt ID/Accession number
	HBP1_HUMAN \| O60381
		Comparative Protein Structure Models	:	ModBase
		Genomic Information	:	Ensembl
		Protein-protein Interaction	:	DIP
		Sequence, Family and Domain Information	:	InterPro \| Pfam \| SMART \| UniProtKB/SwissProt

Access by Enzyme Classificator (EC Number)
	(no 'Enzyme Classificator' available)
		General Enzyme Information	:	BRENDA \| EC-PDB \| Enzyme \| IntEnz
		Pathway	:	KEGG \| MetaCyc

Access by Disease Identifier (MIM ID)
	(no 'MIM ID' available)
		Disease Information	:	OMIM

Access by GenAge ID
	0071
		Age Related Information	:	GenAge

Analysis Tools

Access by PDB/NDB ID
		Domain Information	:	XDom
		Interatomic Contacts of Structural Units	:	CSU
		Ligand-protein Contacts	:	LPC
		Protein Cavities	:	castP
		Sequence and Secondary Structure	:	PDBCartoon
		Structure Alignment	:	STRAP(Java WebStart application, automatic local installation, requires Java; full application with system access!)
		Structure and Sequence Browser	:	STING

Access by UniProt ID/Accession number
	HBP1_HUMAN \| O60381
		Protein Disorder Prediction	:	DisEMBL \| FoldIndex \| GLOBPLOT (for more information see DisProt)

Related Entries

Entries Sharing at Least One Protein Chain (UniProt ID)

UniProtKB/Swiss-Prot
	HBP1_HUMAN \| O60381	:	3qve

Related Entries Specified in the PDB File

(no "Related Entries Specified in the PDB File" available for 2E6O)